/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview is free software: you can redistribute it and/or
 * modify it under the terms of the GNU General Public License 
 * as published by the Free Software Foundation, either version 3
 * of the License, or (at your option) any later version.
 *  
 * Jalview is distributed in the hope that it will be useful, but 
 * WITHOUT ANY WARRANTY; without even the implied warranty 
 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 * PURPOSE.  See the GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.analysis.scoremodels;

import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;

import org.testng.Assert;
import org.testng.annotations.Test;

public class FeatureScoreModelTest
{
  public static String alntestFile = "FER1_MESCR/72-76 DVYIL\nFER1_SPIOL/71-75 DVYIL\nFER3_RAPSA/21-25 DVYVL\nFER1_MAIZE/73-77 DVYIL\n";

  int[] sf1 = new int[] { 74, 74, 73, 73, 23, 23, -1, -1 };

  int[] sf2 = new int[] { -1, -1, 74, 75, -1, -1, 76, 77 };

  int[] sf3 = new int[] { -1, -1, -1, -1, -1, -1, 76, 77 };

  @Test(groups = { "Functional" })
  public void testFeatureScoreModel() throws Exception
  {
    AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded(
            alntestFile, FormatAdapter.PASTE);
    AlignmentI al = alf.getViewport().getAlignment();
    Assert.assertEquals(al.getHeight(), 4);
    Assert.assertEquals(al.getWidth(), 5);
    for (int i = 0; i < 4; i++)
    {
      SequenceI ds = al.getSequenceAt(i).getDatasetSequence();
      if (sf1[i * 2] > 0)
      {
        ds.addSequenceFeature(new SequenceFeature("sf1", "sf1", "sf1",
                sf1[i * 2], sf1[i * 2 + 1], "sf1"));
      }
      if (sf2[i * 2] > 0)
      {
        ds.addSequenceFeature(new SequenceFeature("sf2", "sf2", "sf2",
                sf2[i * 2], sf2[i * 2 + 1], "sf2"));
      }
      if (sf3[i * 2] > 0)
      {
        ds.addSequenceFeature(new SequenceFeature("sf3", "sf3", "sf3",
                sf3[i * 2], sf3[i * 2 + 1], "sf3"));
      }
    }
    alf.setShowSeqFeatures(true);
    alf.getFeatureRenderer().setVisible("sf1");
    alf.getFeatureRenderer().setVisible("sf2");
    alf.getFeatureRenderer().setVisible("sf3");
    alf.getFeatureRenderer().findAllFeatures(true);
    Assert.assertEquals(alf.getFeatureRenderer().getDisplayedFeatureTypes()
            .size(), 3, "Number of feature types");
    Assert.assertTrue(alf.getCurrentView().areFeaturesDisplayed());
    FeatureScoreModel fsm = new FeatureScoreModel();
    Assert.assertTrue(fsm.configureFromAlignmentView(alf
            .getCurrentView().getAlignPanel()));
    alf.selectAllSequenceMenuItem_actionPerformed(null);
    float[][] dm = fsm.findDistances(alf.getViewport().getAlignmentView(
            true));
    Assert.assertTrue(dm[0][2] == 0f,
            "FER1_MESCR (0) should be identical with RAPSA (2)");
    Assert.assertTrue(dm[0][1] > dm[0][2],
            "FER1_MESCR (0) should be further from SPIOL (1) than it is from RAPSA (2)");

  }
}